Topology-Aware Modeling of the Full Genome Reveals Stability Determinants in a Small Naked Virus

Understanding how viral genomes are organized under extreme spatial confinement remains a fundamental challenge in structural virology. Icosahedral viruses, despite offering high-resolution capsid structures through cryo-electron microscopy and X-ray crystallography, present a major obstacle: their genomes do not obey icosahedral symmetry and are thus averaged out during standard reconstruction procedures, leaving genome topology largely unresolved. Computational modeling offers a complementary avenue, but existing approaches often rely on simplified polymer representations that fail to capture sequence-specific features and the extreme compaction observed in small DNA viruses. Here, we focus on Porcine Circovirus type 2 (PCV2), a member of the Circoviridae family and one of the smallest autonomous mammalian viruses, which packages a circular ∼1.7 kb single-stranded DNA genome into a ∼20 nm T = 1 icosahedral capsid at one of the highest DNA packing densities found in nature. We introduce an integrative methodology combining AI-based structural prediction, lattice Monte Carlo simulations, and multiscale molecular dynamics to generate and simulate three-dimensional topological models of the complete virions. Our results demonstrate that distinct genome arrangements can produce virions with experimentally indistinguishable external morphologies, yet differ substantially in their internal energies and predicted particle stability. These findings suggest that circovirus populations comprise structurally similar but energetically heterogeneous assemblies, with implications for infectivity, uncoating, and environmental persistence, while providing a generalizable framework for modeling genome topology in other confined viral systems.